Variant report

Variant	rs6466648
Chromosome Location	chr7:117825297-117825298
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:39677208..39679664-chr7:117824087..117825656,2	MCF-7	breast:
2	chr7:116897859..116900656-chr7:117824567..117826449,2	K562	blood:
3	chr7:117825039..117827152-chr7:120589846..120592123,2	MCF-7	breast:
4	chr7:117822159..117825807-chr7:117854196..117858736,4	K562	blood:
5	chr2:234775602..234777791-chr7:117824084..117825749,2	MCF-7	breast:
6	chr7:117824273..117825955-chr7:117864602..117866522,2	MCF-7	breast:
7	chr7:117825257..117827852-chr7:118309009..118311377,2	K562	blood:

Variant related genes	Relation type
ENSG00000071243	Chromatin interaction
ENSG00000106013	Chromatin interaction
ENSG00000171346	Chromatin interaction
ENSG00000224287	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10085904	0.83[EUR][1000 genomes]
rs1015782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10247768	0.86[EUR][1000 genomes]
rs10487392	0.81[EUR][1000 genomes]
rs10953864	0.82[EUR][1000 genomes]
rs11487110	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11542074	0.86[EUR][1000 genomes]
rs11974039	0.80[EUR][1000 genomes]
rs12154684	0.83[EUR][1000 genomes]
rs12537795	0.82[EUR][1000 genomes]
rs12670769	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12706182	0.81[EUR][1000 genomes]
rs1544584	0.85[EUR][1000 genomes]
rs17140984	0.85[EUR][1000 genomes]
rs17141053	0.83[EUR][1000 genomes]
rs2041527	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2058418	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2215628	0.86[EUR][1000 genomes]
rs2286863	0.86[EUR][1000 genomes]
rs33924981	0.86[EUR][1000 genomes]
rs34019303	0.86[EUR][1000 genomes]
rs35218902	0.84[EUR][1000 genomes]
rs35485182	0.83[EUR][1000 genomes]
rs35708505	0.83[EUR][1000 genomes]
rs41944	0.85[EUR][1000 genomes]
rs41965	0.83[EUR][1000 genomes]
rs41981	0.83[EUR][1000 genomes]
rs41992	0.83[EUR][1000 genomes]
rs42488	0.83[EUR][1000 genomes]
rs45604739	0.86[EUR][1000 genomes]
rs4599745	0.83[EUR][1000 genomes]
rs4730837	0.85[EUR][1000 genomes]
rs4730853	0.83[EUR][1000 genomes]
rs5002232	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61328879	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62466471	0.84[EUR][1000 genomes]
rs62466515	0.86[EUR][1000 genomes]
rs62468297	0.83[EUR][1000 genomes]
rs6942513	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6956486	0.82[EUR][1000 genomes]
rs769435	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7779933	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7786233	0.83[EUR][1000 genomes]
rs7799229	0.81[EUR][1000 genomes]
rs9641593	0.85[EUR][1000 genomes]
rs9656259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656260	0.82[EUR][1000 genomes]
rs996726	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv889088	chr7:117744660-117913648	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6466648	LSM8	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117822400-117825600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr7:117822600-117825800	Active TSS	Psoas Muscle	Psoas
3	chr7:117822800-117825400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:117822800-117825600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:117822800-117825600	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr7:117822800-117825600	Active TSS	A549	lung
7	chr7:117823000-117825400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:117823000-117825400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:117823000-117825400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr7:117823000-117825400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:117823000-117825400	Active TSS	Colonic Mucosa	Colon
12	chr7:117823000-117825400	Active TSS	Thymus	Thymus
13	chr7:117823000-117825400	Active TSS	NHDF-Ad	bronchial
14	chr7:117823000-117825400	Active TSS	NHLF	lung
15	chr7:117823000-117825800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:117823000-117825800	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr7:117823000-117826000	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr7:117823000-117826000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:117823200-117825400	Active TSS	Ovary	ovary
20	chr7:117823200-117825400	Active TSS	Right Ventricle	heart
21	chr7:117823200-117826000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr7:117823400-117825400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:117823400-117825400	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr7:117823400-117825400	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr7:117823400-117825400	Active TSS	Fetal Intestine Small	intestine
26	chr7:117823400-117825400	Active TSS	Fetal Stomach	stomach
27	chr7:117823400-117825400	Active TSS	Stomach Smooth Muscle	stomach
28	chr7:117823400-117825400	Active TSS	Hela-S3	cervix
29	chr7:117823400-117825600	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr7:117823400-117825800	Active TSS	Rectal Smooth Muscle	rectum
31	chr7:117823400-117826000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr7:117823400-117826000	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr7:117823400-117826000	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr7:117823400-117826000	Active TSS	Fetal Brain Female	brain
35	chr7:117823400-117826800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr7:117823600-117825600	Active TSS	NH-A	brain
37	chr7:117823600-117826600	Active TSS	K562	blood
38	chr7:117824400-117825800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr7:117824600-117825400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr7:117824600-117825400	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr7:117824600-117825600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr7:117824600-117825600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:117824600-117825800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr7:117824600-117826000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr7:117824800-117825400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:117824800-117825400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr7:117824800-117825400	Weak transcription	Esophagus	oesophagus
48	chr7:117824800-117825400	Weak transcription	Left Ventricle	heart
49	chr7:117824800-117825400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr7:117824800-117825400	Active TSS	HepG2	liver

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